Wrap Positive Cable w/ Battery Relocation?

So you run through a Ford relay so the starter cable isn't hot all the time, wires routed as required.... what do you do for the power feed for the car?

Run it up to the stock pickup point under the hood?

Relocate fuse box in to trunk?

Add additional fuse box in trunk? (And if you do that, do you run the oe fuse box from there or what?)

I ask because some cars just add accessories over stock and want to keep the factory harness.